Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,011,820 C→T 21.5% R416R (CGC→CGT)  rstB → sensory histidine kinase in two‑component regulatory system with RstA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,011,8200CT21.5% 131.9 / 24.6 92R416R (CGC→CGT) rstBsensory histidine kinase in two‑component regulatory system with RstA
Reads supporting (aligned to +/- strand):  ref base C (48/24);  new base T (15/5);  total (63/29)
Fisher's exact test for biased strand distribution p-value = 5.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTACGCGC  >  minE/1011752‑1011884
                                                                    |                                                                
gTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGc                                                                  <  1:1527934/69‑1 (MQ=255)
gTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGc                                                                  <  1:2376078/69‑1 (MQ=255)
gTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGc                                                                  <  1:2174448/69‑1 (MQ=255)
gTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGc                                                                  <  1:915684/69‑1 (MQ=255)
gTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGc                                                                  <  1:1962885/69‑1 (MQ=255)
   cACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCtt                                                                <  1:1575071/68‑1 (MQ=255)
   cACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCtt                                                                <  1:1605804/68‑1 (MQ=255)
   cACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCtt                                                                <  1:2918893/68‑1 (MQ=255)
   cACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCtt                                                                <  1:2095991/68‑1 (MQ=255)
   cACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCtt                                                                <  1:2056576/68‑1 (MQ=255)
        tataGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTtctc                                                             >  1:3336427/1‑66 (MQ=255)
        tataGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCg                                                            >  1:1880235/1‑67 (MQ=255)
        tataGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCg                                                            >  1:1876342/1‑67 (MQ=255)
        tataGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCg                                                            >  1:36576/1‑67 (MQ=255)
        tataGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCg                                                            >  1:2346569/1‑67 (MQ=255)
        tataGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCg                                                            >  1:1107513/1‑67 (MQ=255)
               cTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTgg                                                   >  1:1103791/1‑69 (MQ=255)
                  gCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGcc                                                 >  1:2995116/1‑68 (MQ=255)
                    aaTGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGtt                                              >  1:3055183/1‑69 (MQ=255)
                    aaTGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGtt                                              >  1:2065583/1‑69 (MQ=255)
                    aaTGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGtt                                              >  1:2552909/1‑69 (MQ=255)
                    aaTGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGtt                                              >  1:1396457/1‑69 (MQ=255)
                       gggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTAt                                            >  1:37784/1‑68 (MQ=255)
                       gggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTAt                                            >  1:2928943/1‑68 (MQ=255)
                       gggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTAt                                            >  1:804090/1‑68 (MQ=255)
                       gggCGGTACGGTTAATTGTGACACCAGCGAACT‑GGT‑GTGCCCGCTTCTCGTTTAGCTGGCCGTTATgg                                          >  1:2948225/1‑68 (MQ=255)
                        ggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATgg                                          <  1:897844/69‑1 (MQ=255)
                        ggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATgg                                          <  1:3236631/69‑1 (MQ=255)
                        ggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATgg                                          <  1:1614400/69‑1 (MQ=255)
                             tACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATaa                                     >  1:970717/1‑69 (MQ=255)
                              aCGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAAc                                    >  1:422763/1‑69 (MQ=255)
                              aCGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAAc                                    >  1:1374355/1‑69 (MQ=255)
                              aCGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAAc                                    >  1:2743213/1‑69 (MQ=255)
                              aCGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAAc                                    >  1:1156216/1‑69 (MQ=255)
                              aCGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAAc                                    >  1:1160113/1‑69 (MQ=255)
                              aCGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAAc                                    >  1:3402045/1‑69 (MQ=255)
                                 gTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATc                                 >  1:3289325/1‑69 (MQ=255)
                                 gTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATc                                 >  1:2148068/1‑69 (MQ=255)
                                 gTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATc                                 >  1:3108395/1‑69 (MQ=255)
                                 gTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATc                                 >  1:1328127/1‑69 (MQ=255)
                                 gTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATc                                 >  1:325192/1‑69 (MQ=255)
                                 gTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATc                                 >  1:710562/1‑69 (MQ=255)
                                 gTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATc                                 >  1:959586/1‑69 (MQ=255)
                                 gTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATc                                 >  1:2073920/1‑69 (MQ=255)
                                 gTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATc                                 >  1:2882148/1‑69 (MQ=255)
                                  ttAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATgg                                          <  1:2931867/59‑1 (MQ=255)
                                    taTTGTGTCAGCTGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATgg                                          <  1:119606/56‑1 (MQ=255)
                                        gtgACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCt                                                     >  1:985625/1‑42 (MQ=255)
                                        gtgACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCaa                           >  1:1176313/1‑68 (MQ=255)
                                        gtgACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCaa                           >  1:670884/1‑68 (MQ=255)
                                        gtgACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCaa                           >  1:3393182/1‑68 (MQ=255)
                                        gtgACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCaa                           >  1:3334933/1‑68 (MQ=255)
                                        gtgACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCaa                           >  1:3234234/1‑68 (MQ=255)
                                        gtgACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCaa                           >  1:2789123/1‑68 (MQ=255)
                                        gtgACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCaa                           >  1:186332/1‑68 (MQ=255)
                                           acacCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAAttt                        <  1:2514103/68‑1 (MQ=255)
                                           acacCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAAttt                        <  1:3435107/68‑1 (MQ=255)
                                           acacCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAAttt                        <  1:3176960/68‑1 (MQ=255)
                                           acacCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAAttt                        <  1:2115456/68‑1 (MQ=255)
                                           acacCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAAttt                        <  1:2355540/68‑1 (MQ=255)
                                                 gCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTg                 <  1:3343538/69‑1 (MQ=255)
                                                 gCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTg                 <  1:1363058/69‑1 (MQ=255)
                                                      cTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATcc                                >  1:1414772/1‑49 (MQ=255)
                                                      cTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGa            >  1:47937/1‑69 (MQ=255)
                                                      cTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGa            >  1:2433774/1‑69 (MQ=255)
                                                      cTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGa            >  1:1725592/1‑69 (MQ=255)
                                                        gggTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTg                 <  1:3282895/62‑1 (MQ=255)
                                                                cccGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTa                       <  1:34874/48‑1 (MQ=255)
                                                                cccGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTa                       <  1:1556468/48‑1 (MQ=255)
                                                                cccGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTa                       <  1:242715/48‑1 (MQ=255)
                                                                cccGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTa                       <  1:3303940/48‑1 (MQ=255)
                                                                cccGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTa                       <  1:2784132/48‑1 (MQ=255)
                                                                cccGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTa                       <  1:1359457/48‑1 (MQ=255)
                                                                cccGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTa                       <  1:1512268/48‑1 (MQ=255)
                                                                cccGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTa                       <  1:2018792/48‑1 (MQ=255)
                                                                cccGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTa                       <  1:1236624/48‑1 (MQ=255)
                                                                cccGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTACgcgc  >  1:2307341/1‑69 (MQ=255)
                                                                cccGCTTCTCGTTTAGCTGGCCGTTATGCCATAACATCCCGCAATTTa                       <  1:1769326/48‑1 (MQ=255)
                                                                cccGCTTCTCGTTTAGCTGGCCGCTATGGCATAACATCCCGCAATTTa                       <  1:3235522/48‑1 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGGATAACATCCCGCAATTTACCTCTGc                >  1:2636454/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGTAATTTACCTCTGc                >  1:1630169/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTg                 >  1:143688/1‑52 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:1247083/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:1238265/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:118147/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:2500411/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:143156/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:266508/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:3373826/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:336567/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:332538/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:3109342/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:3069902/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:3010405/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:2022562/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                >  1:2212578/1‑53 (MQ=255)
                                                                  cGCTTCTCGTTCAGCTGGCCGTTATGGAATAACATCCCGCAATTTACCTCTg                 >  1:2134905/1‑52 (MQ=255)
                                                                    |                                                                
GTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTACGCGC  >  minE/1011752‑1011884

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A